Hoffman2:Scripts:setup subject 3: Difference between revisions
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--config filename | --config filename | ||
specifying the bids naming configuration file path and name. Users should generate this file based on their data and Bids formatting rule. However there are sample files. | specifying the bids naming configuration file path and name. Users should generate this file based on their data and Bids formatting rule. However there are sample files. | ||
--sessdir ses-NN | |||
specify session directory name. This is for Bids format mode and when the data has multiple sessions. When you want the results all go into a session directory named ses-NN (NN represents session number, e.g. 02) | |||
===Examples: === | ===Examples: === |
Revision as of 23:30, 16 October 2019
Setup_subject script usage
Setup_subject_3 is built on top of setup_subject_2. The major goal is to apply BIDs format on the data structure. Besides of using BIDs structure, it added other useful features as well.
Setup_subject_3 has all the functions which exist in setup_subject_2 and works the same way with the same options as setup_subject_2.
Basic Usage:
setup_subject_3 [option] basedir subjectID
basedir is where you want the processed data to be stored in your Hoffman account,
subjectID is the subject folder name which has your subject Dicom data
Options:
--download hostname,userid,path
download data from Dicom server to you hoffman account It requires 3 argument, separated by comma(,) (If you have downloaded the data already, this option is not needed)
1. hostname - (ccn for ccn Dicom server, bmap for BMC Dicom server). 2. userid: Your Dicom server user ID 3. path: path to your data in dicom server
-d (or --do) : this option to specify the processing you want to add
After NIFTI convert, these options can be used to run FSL mcflirt, bet and melodic also diag, and mprage.
mcflirt : run mcflirt bet : run bet melodic : run melodic diags : run diagnostics mprage : process anatomical scans sge: submit the job in batch mode
(Using option diags requires mcflirt, bet and melodic to be processed first)
-s (or --skip)
this option to specify the processing you want to skip
mcflirt : run mcflirt bet : run bet melodic : run melodic diags : run diagnostics mprage : process anatomical scans sge: not using batch mode, which means you need to start interactive mode first before running setup_subject_* command
--spm
Set SPM compatability
--bids
Bids format: specify using bids structure to group result files. However this option often being used with --config option to choose configuration file. Without configuration file, the name conversion might not be correct under BIDs format rule.
--config filename
specifying the bids naming configuration file path and name. Users should generate this file based on their data and Bids formatting rule. However there are sample files.
--sessdir ses-NN
specify session directory name. This is for Bids format mode and when the data has multiple sessions. When you want the results all go into a session directory named ses-NN (NN represents session number, e.g. 02)
Examples:
Load the script module first:
module load ccnscripts
Download data and run NIFTI convert
setup_subject_3 --download ccn,dicomuserid,/dicom/data/YOURGROUP/ basedir subjectID
( /dicom/data/YOURGROUP/subjectID should be where the raw data is located and accessable by your Dicom server user account)
Download data and run NIFTI convert and other FSL processing:
setup_subject_3 --download ccn,userid,/dicom/data/YOURGROUP/ -d mcflirt,bet,melodic,diags,mprage --spm basedir subjectID
Process data only without download
setup_subject_3 -d mcflirt,bet,melodic,diags basedir subjectID setup_subject_3 -d mcflirt,bet,melodic,diags,mprage basedir subjectID setup_subject_3 -d mprage basedir subjectID
Skip mcflirt,bet,melodic,diags
setup_subject_3 -s mcflirt,bet,melodic,diags basedir subjectID
Notes
Log File: provides useful details about what commands were run, their output and the script's status. It's located at
basedir/subjectID/notes/setup_log.date_numbers